Project Summary/Abstract Core E ? The Genomics and Sequencing Core (GS Core) is a laboratory based service Core designed to facilitate HIV research involving genomics technologies. The GS Core provides an easy and efficient path for SD Center for AIDS Research (SD CFAR) investigators to incorporate sophisticated genomics technologies such as next generation sequencing (NGS), digital droplet PCR (dPCR) and single-cell genetic characterization into their research activities. The specific aims of the GS Core are to: Aim 1. Develop and provide molecular tools and resources for the determination of host and viral mechanisms of pathogenesis (e.g. gene expression, viral quantitation, host and viral variation, copy number, HIV integration assays, full-length pol and env sequencing, and other resources needed by the SD CFAR community); Aim 2. Assist researchers in the value, use and interpretation of genetic information and gene expression data (e.g. analysis of gene expression and sequence variation, application of software tools for alignment, phylogeny and other sequence comparisons); Aim 3. Facilitate education and training in genomics technologies for investigators, trainees, staff, and other researchers (e.g. seminars and workshop presentation, participation in CFAR activities including Scientific Working Group (SWG) meetings, individual training for graduate students, postdoctoral fellows and emerging investigators learning genomics technologies, assist and direct users to reagents and materials useful in HIV research). Overall, ?State of the Art? is ever changing for genomics and sequencing technology. To provide the most useful and up-to-date services, the GS Core will monitor and anticipate the evolving needs of CFAR investigators through user feedback, survey, evaluation of the directions of the community in meetings and presentations, and incorporating recommendations from internal and external advisory committees and reviews. Immediate challenges that are addressed in this application include: 1. Support of single-cell sequencing technologies, 2. Facilitation of access to existing and planned pipelines for analysis of viral variation, antiretroviral resistance, and viral integration, 3. Further development of long-read sequencing technologies, and 4. ?Hands On? workshops for CFAR investigators to foster a working knowledge of scripting and analysis of phylogeny, expression, variation, and other topics.